IMHO, putting the panel lines and rivets on top of the paint just looks wrong. It makes them WAY too obvious. I spent a number of years building and repairing real planes so I kinda think I know what I'm talking about here
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In real life, fixed skin panels have a gap of about 1/8" between them. However, this gap is almost always filled with a rubbery sealant that makes the gap essentially flush with the metal on both sides. This sealant is put on both to smooth out the skin for aerodynamics and to keep water out. Paint goes over this sealant, so on painted planes the fixed panel lines are nearly invisible. There's just a very small surface discontinuity that catches just a tiny bit more light or shadow than the surrounding skin. Unless the light's hitting at just the right angle, you don't see fixed panel lines at all on painted planes.
The sealant between the panels is usually black. Thus, on unpainted planes, you have very fine black lines all around the fixed skin panels. But even so, you shouldn't have any 3D effect on them, because the sealant is level with the sheet metal. So fixed panel lines should never look like trenches, nor should they ever appear as black on painted planes.
There are a couple of exceptions to the above. Some fixed skin panels are thicker than their surroundings. Examples are doublers, patches over damage, etc. Because these stand proud of the surface, you have a definite step around their edges, so a 3D look is appropriate. Also, early-war Russian planes often didn't have sealant in any gaps, while very late-war German planes often didn't have sealant at major sub-assembly joints due to shortages and time constraints. An example of the latter is where the tail unit joins the fuselage on the Dora. These parts were built in separate factories and each major chunk had its gaps sealed, but the joints between them were often just heavily oversprayed with dark paint instead of having sealant.
Lines around removeable panels (engine cowlings, gunbay doors, inspection panels, etc.) are much more visible. Usuually, these panels get bent slightly from repeated used so don't seal up tight after a while. So you'd have some 3D effect around their edges here and there, plus usually a distinct 3D gap between them and the surrounding fixed panels.
Most WW2 planes had flush rivets. These are even more invisible than fixed panel lines in most cases, so on painted planes really ain't worth the bother of doing. The fastener head is within a few thousandths of an inch of being flush, so primer and topcoat paint usually totally obsucre them. On unpainted planes, the flush rivets catch the light slightly differently so are just barely visible.
Again, there are exceptions. Late-war German planes often weren't built very well (****-eyed rivets and the skin dented in around them), nor were they given as many or as thick coats of paint. So their rivets, especially on the fuselage, were sometimes fairly visible. Also, on any plane, the harder the curve of the sheet metal, the less the flush rivet head matches the contour, so the more distinct it is in the proper lighting condtions. Finally, all planes had a few dome-head rivets here and there, especially where the sheet metal was VERY thing like around the tail. Or around damage patches. But for the most part, rivets ain't worth the trouble of doing.
